Matrix indexing seems to give rather "variable" results when zeros or
negative values are included among the indices (in terms of both error
messages and in terms of the number of returned values when there is no
error message).

Is this the intended behavior?

I couldn't see any comments about zeros or negative values in matrix
indices in either ?"[" or Section 3.4.2 "Indexing matrices and arrays"
of the "R Language Definition" (Version 2.0.1), or in Section 5.3 "Index
arrays" of "An Introduction to R" (Version 2.1.0).

(It looks like the special treatment of zeros and negative indices is
being applied to the vector indices after they are derived by standard
indexing arithmetic from the matrix indices -- so zeros and negative
values in the matrix indices have no special meaning. There does seem
to be some range checking, but it's not consistent -- sometimes index
values that are out of range get through.)

PS: FWIW, S-PLUS 6.2 does something more like one would get when using
each row of the index matrix as arguments to a call to "[", except that
negative values are not allowed at all (any zero value in a row causes
that row to be omitted from the result).